About mentioning your low grades: I've noticed some schools, in their SOP prompts, actually say that it's a space where you can explain anomalies in your GPA/GREs, etc. So if they say that, do it. Just make sure to explain it as something you got over: "I was upset in 200X by an assault and my grades in that term suffered, but as you can see, I wave worked past that: since then I have maintained a much higher GPA, presented at conferences, etc.". I'd second that it's good to have a prof mention it also/in more detail.